Biofilm remediation of fracture fluid

ABSTRACT

A method of in situ treatment of fracture fluid that is contaminated with a heavy metal may include passing a flow of contaminated fracture fluid through a reactor vessel. The reactor vessel may contain a plurality of biofilm retaining structures. Each of the structures may at least be partially coated with a biofilm. Additionally, the biofilm may include a plurality of bacteria retained in a matrix and the matrix may include DNA, protein and carbohydrates produced by the bacteria.

CROSS-REFERENCE TO RELATED APPLICATIONS

This patent application claims priority to co-pending U.S. Provisional Patent Application No. 61/219,239, entitled “Biofilm Remediation of Fracture Fluid”, filed on Jun. 22, 2009 and U.S. Provisional Patent Application No. 61/219,249, entitled “Biofilm Remediation of Metal-Containing Wastewater”, filed on Jun. 22, 2009, each of which are incorporated herein by reference in their entireties.

BACKGROUND

The Marcellus Shale, a member of the Devonian Black Shales, is the largest known deposit of natural gas in the United States. It extends from Ohio and West Virginia, through Pennsylvania and into Southern New York, an area of 54,000 square miles, which is several times the size of the Barnett Shale. The Marcellus Shale has the potential to fulfill America's natural gas needs for years to come.

Hydraulic fracturing is a process whereby fluid under pressure is used to fracture open the shale, such as that in the Marcellus Shale, to greatly enhance the recovery of natural gas. The fluid used in hydraulic fracturing (often referred to as “fracture water,” “frac water” or “frac fluid”) is primarily water. Other components of frac fluid may include sand proppant, hydrochloric acid, glutaraldehyde as a biocide, sodium chloride, ethylene glycol and various components for scale inhibitor and iron control. The exact composition of frac fluid may vary.

One of the properties of frac fluid is that it is very viscous in order to carry the proppant (sand) into the cracks in the rock. To make the fluid viscous enough, polymers (usually carbohydrates) are added to the frac fluid. Frac fluid unavoidably picks up metals from the deep formations. Some of these metals may be toxic (e.g., arsenic) and/or radioactive (e.g., uranium).

Disposal of the flow-back water (frac fluid) is one of the biggest challenges facing the recovery of natural gas from shale. Each well can produce millions of gallons of flow-back water, because after the fracturing process about 60% of the water used is pushed back up the well by the released gas. Ground water can be protected by casing, but the problem lies in the safe disposal of the flow-back water which can contain arsenic, manganese, cobalt, chromium, lead, various other metals and dissolved wastes, as well as compounds added by the manufacturer. An additional concern is that the frac fluid can be radioactive from Radium 226 and Radium 228.

Current disposal methods are unsatisfactory for environmental or economic reasons and do not provide for the recycling of the frac fluid. These disposal methods include: diluting the fluid with sewer effluent and discharging it into a river or stream or trucking the waste to industrial water treatment facilities.

The methods and systems described in this document are directed to treatment of fracture fluid that is contaminated with heavy metals.

SUMMARY

In one embodiment, a method of in situ treatment of fracture fluid that is contaminated with a heavy metal is described. In certain embodiments, the method comprises passing a flow of contaminated fracture fluid through a reactor vessel. The reactor vessel may contain a plurality of “biofilm retaining structures”. Such structures may be in any shape or form such as, but not limited to saddles, spheres, cubes, nut shells or combinations thereof. These structures are utilized to enlarge the surface area that the biofilm grows on and may provide nutrients and supply to the bacteria. Each of the structures may at least be partially coated with a biofilm. Additionally, the biofilm may include a plurality of bacteria retained in a matrix and the matrix may include DNA, protein and carbohydrates produced by the bacteria.

In one embodiment, the biofilm may be grown on nut shells such as, but not limited to, walnut shells, pistachio shells, peanut shells or combinations thereof.

In yet another embodiment, the metal includes, but not limited to, cadmium, iron, nickel, radium, uranium, cobalt, lead, manganese, and arsenic. In one embodiment, the biofilm is inert with respect to the fluid. Additionally, the matrix is electrostatically charged, which attracts the metals and draws them into the matrix.

In selected embodiments, the bacteria that are used for bioremediation include at least one of the following genera: Pseudomonas, Aeromonas, Klebsiella, Bacteroides and a combination thereof.

In yet another embodiment, the bacteria that are used for bioremediation include at least one of the following: Deinococcus geothermalis, and Deinococcus radiodurans.

In another embodiment, the bacteria that are used for bioremediation include at least one of the following: Vibrio proteolyticus, Shewanella piezotoleran, Shewanella Baltica and combinations thereof. In another embodiment, the bacteria that are used for bioremediation may include: Pantoea agglomerans, Vibrio vulnificus and combinations thereof.

In yet another embodiment, a site specific method for biofilm remediation of contaminated fracture fluid includes: isolating endemic microbes from the heavy metal contaminated fluid; screening the endemic microbes for heavy metal reduction and removal; selecting cultures of heavy metal removal organisms; optimizing the cultures for heavy metal reduction and removal; and establishing a high density biofilm of the heavy metal reducing organisms within a reactor.

BRIEF DESCRIPTION OF THE DRAWINGS

For a fuller understanding of the nature and advantages of the present embodiments, reference should be made to the following detailed description taken in connection with the accompanying drawings.

FIG. 1 depicts an exemplary structure of a reactor vessel.

FIG. 2 depicts an exemplary structure of a group of “saddles” on which bacteria can grow.

DETAILED DESCRIPTION

Before the present compositions and methods are described, it is to be understood that this invention is not limited to the particular processes, compositions, or methodologies described, as these may vary. It is also to be understood that the terminology used in the description is for the purpose of describing the particular versions or embodiments only, and is not intended to limit the scope of the present invention which will be limited only by the appended claims. All publications mentioned herein are incorporated by reference in their entirety. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.

As used herein, and in the appended claims, the singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise. In addition, the word “comprising” as used herein is intended to mean “including but not limited to.” Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art.

As used herein, all claimed numeric terms are to be read as being preceded by the term, “about,” which means plus or minus 10% of the numerical value of the number with which it is being used. Therefore, a claim to “50%” means “about 50%” and encompasses the range of 45%-55%.

Shale formations are fractured using water or engineered fluids to release natural gas. Such fluids are used to split the rocks and to carry proppant (sand) into the fissures to hold them open. These fluids are in intimate contact with the rocks and, unavoidably, pick up metal ions that are potentially toxic to humans and/or have deleterious effects to the environment. The fracture fluids that are recovered following the extravasation process have similar properties as those that were injected at the outset, with the exception of the acquisition of many metals, and some salt (NaCl).

The methods and systems described in this document are directed to a biofilm-based bioremediation technology that removes impurities such as heavy metals from the recovered frac fluid that may be at or near the site of its recovery. This method may allow the frac fluid to be recycled. Bioremediation is any process that uses microorganisms, fungi or plants to return the natural environment altered by contaminants to its original condition. This process allows for reconditioning of flow-back frac fluid for reuse. Bioremediation of many synthetic or organic compounds is carried out by indigenous microorganisms, principally heterotrophic bacteria, which transform contaminants to intermediate products, innocuous end products or immobilized substances.

We have discovered that recovered fracture fluids may be passed through a biofilm that removes heavy metals from the fluid and captures the metals. The bacterial genera that are used for bioremediation may include at least one of the following genera: Pseudomonas, Aeromonas, Klebsiella, Bacteroides and a combination thereof. Specific bacterial strains that may be used for bioremediation include Deinococcus geothermalis, Deinococcus radiodurans and combinations thereof which are radiation and heat resistant. The genome of Deinococcus geothermalis has been sequenced and has been designated a GenBank Accession ID: CP000359. The genome of Deinococcus radiodurans has been sequenced with designated GenBank Accession ID: AE000513.1 for Chromosome 1, GenBank Accession ID: AE001825.1 for Chromosome 2, GenBank Accession ID: AE001827.1 for R1 plasmid CP1, and GenBank Accession ID: AE001826.1 for plasmid MP1. The genome of metal-reducing bacteria named Geobacter FRC-32 has been sequenced with designated GenBank Accession ID: CP001390.

In one embodiment, specific cultivated bacterial strains and natural bacterial enrichments may be selected that favor the formation of biofilms with optimal metal binding capabilities.

In another embodiment, the bacteria that are used for bioremediation include at least one of the following: Vibrio proteolyticus, Shewanella piezotolerans (with designated GenBank Accession ID: CP000472), Shewanella baltica (with designated GenBank Accession IDs: AM743169, CP001252, CP000753, CP000891, and CP000563) and combinations thereof. In another embodiment, the bacteria that are used for bioremediation may include: Pantoea agglomerans, Vibrio vulnificus (with designated GenBank Accession IDs: AE016795 and AE016795) and combinations thereof.

In certain embodiments, the bacteria may be modified with a tag, barcode or other genetic identifier to allow for identifying the source of biofilm. Tagging and barcoding of bacteria can be done by any method known to one skilled in the art such as, but not limited to, by genetic modifications, fluorescent labeling and unique identifier polymers. In yet another embodiment, tagging and/or barcoding of bacteria allows for detection of maturation of biofilm. In such methods unique identifiers such as, but not limited to, genetic modifications, fluorescent labeling and unique polymers are utilized to signal the maturation of biofilm for efficient remediation of fracture fluid. When bacteria are modified to include an identifier, the identifier will be reproduced as the biofilm grows in the vessel. As used in this document, a general reference to a bacteria is intended to include both the unchanged bacteria and a bacteria that is so modified with an identifier.

A biofilm includes one or more bacteria strains disposed in a matrix containing extracellular polymeric substances such as DNA, protein and/or carbohydrates, some of which may be produced by the bacteria. Growth in biofilms allows bacteria to remain stationary in any porous ecosystem (i.e., soil), and to trap nutrients and metals through their water channels. The trapping system derives from the characteristics of the bacterial extracellular polysaccharide (EPS) matrix, which is composed largely of uronic acid (sugar molecules with two carboxylic acid moieties that impart an overall negative charge). Thus, the EPS matrix acts as an ion exchange material that immobilizes positively charged molecules or ions that penetrate through the water channels. In some embodiments, the matrix may make up about 85% by volume of the film, while the bacteria strains may make up about 15% by volume of the film. Other ranges are possible. For example, the matrix may make up about 50% by volume of the film, the matrix may make up about 60% by volume of the film, the matrix may make up about 70% by volume of the film, the matrix may make up about 80% by volume of the film, or the matrix may make up about 90% by volume of the film.

Biofilms provide structures to trap radioactive materials and other heavy metals. Biofilms may be encased in a polysaccharide matrix (also known as “slime”) that surrounds the bacteria and, in some embodiments, makes up about 85% of the volume of biofilms. The matrix may include an anionic polymer. Anionic polymers are molecules with an enormous affinity for metals and may be co-polymers of acrylamide with increasing contents of acrylic groups, which give the polymers their negative charges. An example of an anionic polymer includes, but is not limited to, uronic acids such as alginates. Additionally, fully charged matrices can trap negative particles via their bound positively-charged metal ions.

In yet another embodiment, biofilms may be formed on suitable surfaces also referred to as “biofilm retaining structures” such as, but not limited to, saddles, spheres, cubes, nutshells and combinations thereof to establish “bed reactors”. A bed reactor is a container or vessel containing a number of biofilm or coated a structure through which wastewater is passed.

FIG. 1 illustrates an exemplary reactor vessel 10 for treating flow-back fracture fluid from hydraulic fracturing. The vessel 10 includes a tank structure 15 which may be made of glass, ceramic, or another material that is resistant to corrosion. An intake opening 42 may be connected to input tube 40 for delivery of fluid into the tank structure. An output tube 50 may be connected to an outlet opening 52 for the transmission of fluid that exits the tank structure. The tank structure holds a biofilm retaining structure 20, and a biofilm 30 wherein the input tube, output tube, the biofilm retaining structure and the biofilm are configured so that the fracture fluid is uniformly exposed to the biofilm while in the vessel.

The biofilm retaining structures are any structures that provide surface area on which the biofilm may attach and grow. The structures may be glass, ceramic, or an organic material. Examples include saddle-shaped ceramic structures such as those shown in FIG. 2, glass beads, other structures shaped as spheres, cubes or other shapes, organic material such as nut shells, or combinations any of these items.

Before the reactor vessel is used to treat fracture fluid, the biofilm must be grown in the tank structure. To do this, the desired bacteria may be introduced into the vessel, either directly from a cultivated strain, or indirectly by passing fracture fluid or other fluid that contains the bacteria into the vessel. The bacteria will attach to the retaining structures and grow over a period of time. Fluid will be retained in the vessel to support growth, and the fluid may include material that will enhance the growth such as sugar, organic matter, or other material to promote reproduction of the bacterial. In some embodiments, the biofilm (bacteria in a matrix) may be allowed to grow until it achieves a thickness of about 50 microns or more over substantially all of the retaining structures. Alternatively, it may be allowed to grow until the bacteria make up about 10% by volume of the film, about 15% by volume of the film, about 20% by volume of the film, about 30% by volume of the film, about 40% by volume of the film, or about 50% by volume of the film. Other percentages and ranges are possible, including but not limited to all numbers between the percentages described above.

In another embodiment, the reactor vessel may further include or be in connection with a one-way valve 60 connected to the outlet tube to prevent re-entry of the fluid into the outlet tube 50 after the fluid passes through the valve. In yet another embodiment, the reactor vessel may further include or be connected to a flow regulator 70 that limits the flow rate of the fluid into the chamber. Fracture fluid may contain biocides such as glutaralderhyde (1,5-pentanedial) to control bacterial activity. However, such biocides are not desirably introduced into a reaction vessel such as that disclosed herein. In such situations, before the fracture fluid is introduced into the reaction vessel, the fluid may be passed through a treatment vessel where the glutaralderhyde or other biocide may be removed, such as by chemical neutralization. Alternatively, the biofilm may be given additional time to acclimate to the biocide. Acclimation times and conditions have been shown in, for example, Laopaiboon et al., “Effect of gluteraldyhyde biocide on laboratory-scale rotating biological contactors and biocide efficiacy,” Electronic Journal of Biotechnology, vol. 9, no. 4 (Jul. 15, 2006).

The biofilm may include or be produced by a bacteria that removes a heavy metal such as cadmium, iron, nickel, radium, uranium, radium, cobalt, lead, manganese, arsenic or combinations thereof. For example, the bacteria may include at least one of the following: Deinococcus geothermalis, Deinococcus radiodurans and combinations thereof.

FIG. 2 shows a group of saddles made of a ceramic or other inert material on which a biofilm may grow as biofilm retaining structures. The saddle may be made of a material that does not react with the biofilm, such as glass or ceramic. Alternatively, the retaining structures may be made of an organic material, such as nut shells, that provides nutrients to the biofilm.

In an embodiment, a method of treating fracture fluid from hydraulic fracturing of shale includes collecting flow back fracture fluid from fractured shale; passing the fracture fluid through a reactor vessel to remove one or more heavy metals from the fracture fluid; and reusing the fracture fluid in another shale fracturing operation. In an embodiment, reusing the fracture fluid may comprise introducing the fracture fluid back in the natural resource after heavy metal removal. The heavy metal may include, for example, cadmium, iron, nickel, radium, uranium, cobalt, lead, manganese or arsenic.

Very large volumes of fracture fluid can be passed through these fixed bed reactors. The biofilms may separate virtually all of the metal ions from the water as long as two conditions are maintained: 1) Biocides that are routinely used to control bacterial activity in fracture fluids may be partially or completely removed. These organic compounds (typically glutaralderhyde) are usually removed by chemical neutralization. 2) Fluidized bed reactors must be used if there is a significant tendency to plug the reactor with either the fluid being processed, or with biofilm growth in response to the presence of organic nutrients in the fluid. Fixed bed reactors may be used if the viscosity of the fluid being treated is such that boundary plugging can be obviated. Metals may be precipitated by the chemical and physical conditions inside the bioreactor, in which pH changes may render certain metals to be insoluble, and the valences of some metals may be changed by oxidizing or reducing conditions.

Metal removal may be measured by atomic adsorption until the optimal level of removal is obtained. When a high degree of metal removal has been obtained (i.e., up to 100% removal), the microbial population on the biofilm retaining structures may be analyzed by the Ibis method or another method, and the species composition of the microbial population that shows the best metal removal kinetics may be recorded. In such a manner, one may determine an appropriate microbial species to target removal of a particular metal.

Heavy metals that may be removed by the methods and systems described above include, but are not limited to, cadmium, iron, nickel, radium, uranium, cobalt, lead, manganese and arsenic. The microbial biofilms may trap metallic ions and remove toxic metals from fracture fluids.

In one embodiment, bioremediation may occur as the water passes through the biofilm. The biofilm may convert the metals to valence states in which they are non-toxic and/or insoluble so that they can be disposed of in safer and more economical manners. An example is the conversion of uranium from the mobile 2× valence to the 6× valence in which it is a fine, black, insoluble precipitate. The remediation may not “destroy” the metal, but the bacteria may convert the metals from one valence state to another. This conversion, in turn, provides energy for bacterial metabolic processes. The trapping system may arise at least in part from the characteristics of the extracellular matrix. For example, a matrix that substantially includes uronic acids, which are sugar molecules with two carboxylic acid moieties that impart an overall negative charge, may act like an ion exchange material. Such a material would immobilize any positively charged molecules or ions that penetrate its open water channels. Fully charged matrices can even trap negative particles via their bound positive metal ions.

In one embodiment, biofilms and their derivatives may act as molecular “sponges” for trapping heavy metals in frac fluid. Even without full knowledge of the chemical composition of fracture fluid, biocides present in frac fluid can be neutralized with chemicals. The fluid is then passed through biofilm reactors very similar to those used in “pump and treat” operations to bioremediate subsurface plumes of organic pollutants. These biofilm reactors trap most metals and alter the valence states of them to produce insoluble deposits from soluble entities.

The bed reactors described herein may be transportable, and may be used in situ, such as on the site where the wastewater removal occurs. For example, a multispecies biofilm may be grown on the surface of a truck-mounted reactor. After neutralization of biocides, contaminated frac fluid is pumped through a bioreactor. Metals bind to the biofilm and are removed from the frac fluid. The treated frac fluid is then metal-free and can be pumped and reused without hazard to anyone.

Once the metal composition in the contaminated frac fluid is known, specific bacteria may be selected for the biofilm to allow for efficient containment of each metal (e.g., Schewanella that makes 6× valence uranium). Thus, unique, site-specific, complex polymicrobial communities and other bioremediation solutions may be applied based on the decontamination needs of individual sites, as not all sites produce the same set of waste products. The advantage of this technique is the ability to first characterize the contamination at a molecular level and then develop targeted approaches to bioremediate efficiently. Because the undersirable elements that are acquired by fracture fluids are metals, the simple removal of these metals will make these fluids suitable for re-use or for safe disposal. If toxic metals are absent from recovered fracture fluids, excess salt can be recovered by distillation, and safely used for many routing applications (e.g., salting roads in winter).

After bioremediation, polymers in the frac fluid may be largely unchanged, so that the fluid (minus metals) can be reused or subject to other remediation processes. After many uses, the truck-mounted bioreactor may be driven to a specific location; the biofilms may be dissolved with bleach, an antibacterial compound, an antifungal compound or combinations thereof. The metals may be recovered for commercial exploitation or safe disposal. The biofilm retaining structures may then be used to regenerate new biofilms for re-use of the reactor.

In one embodiment, the biofilm may be regenerated after several days of use. In certain embodiments, the biofilm may be regenerated after the efficiency of metal uptake falls below 80%. In yet another embodiment, the biofilm may be regenerated after the efficiency of metal uptake falls below 70%. In another embodiment, the biofilm may be regenerated after the efficiency of metal uptake falls below 60%.

In one embodiment, methods of destroying and regenerating biofilm retaining structures using a biocide may be used. Biocides may be used to destroy biofilms after several use or when the biofilm reaches saturation from metal uptake. In one embodiment, the biofilm may be regenerated after the efficiency of metal uptake falls below 80%. In yet another embodiment, the biofilm may be regenerated after the efficiency of metal uptake falls below 70%. In another embodiment, the biofilm may be regenerated after the efficiency of metal uptake falls below 60%.

The biocide may include bleach, antibacterial, antifungal and compositions thereof. In certain embodiments, 5% v/v bleach is used for about 4 hours to digest the biofilm. It may take up to about 1 week to regenerate the biofilm. In an embodiment, bacteria are inoculated and grown in a medium containing nutrients such as, but not limited to, tripticase soy broth.

The biofilm reactors can be mounted on a vehicle such as a truck, so that effective bioremediation can allow the local re-use of fracture fluid in the field. An exemplary reactor may have a tank that is about 3 meters in diameter and about 2 meters high. In addition, the efficiency of the treatment can be monitored by flame photometry, so that this re-use can be virtually immediate.

EXAMPLE

A biofilm may be formed in a glass reaction vessel having a volume of approximately 10 liters. The vessel may be filled to the half or ⅔ level with ceramic saddles having an average maximum dimension of 6 mm. A spoonful of soil from a location that has been exposed to flow-back fracture fluid may be added to the vessel, and approximately 50 ml of the fluid may be collected and added to the vessel. The fluid may be slowly cycled through the vessel until a biofilm grows on the saddles to form a film that is visually observed to substantially cover the exposed surfaces of the saddles. For example, the fluid may be cycled through 30-50 times, with each cycle allowing the fluid to be exposed to the film for about 8-10 minutes. After the film is formed in this manner, additional fracture fluid may be collected and passed through the vessel for metals removal at a flow rate that allows the fluid to be exposed to the biofilm for at least 8-10 minutes.

It will be appreciated that various of the above-disclosed and other features and functions, or alternatives thereof, may be desirably combined into many other different systems or applications. It will also be appreciated that various presently unforeseen or unanticipated alternatives, modifications, variations or improvements therein may be subsequently made by those skilled in the art which are also intended to be encompassed by the disclosed embodiments. 

1. A method of treating fracture fluid from hydraulic fracturing of shale comprising: collecting flow back fracture fluid from a fractured shale; passing the fracture fluid through a reactor vessel to remove one or more heavy metals from the fracture fluid, the reactor vessel containing a plurality of biofilm retaining structures, wherein each of the structures is at least partially coated with a biofilm; and reusing the fracture fluid in a gas shale.
 2. The method of claim 1 wherein the biofilm comprises a plurality of bacteria retained in a matrix produced by the bacteria.
 3. The method of claim 1, further comprising, before the collecting: introducing soil that has been exposed to the fracture fluid into the vessel; collecting an amount of fracture fluid; cycling the fracture fluid through the vessel until the biofilm grows on the retaining structures to a level that is sufficient to remove the one or more heavy metals from the fracture fluid.
 4. The method of claim 1, wherein reusing the fracture fluid comprises introducing the fracture fluid back in a natural resource after heavy metal removal.
 5. The method of claim 1, wherein the heavy metal comprises cadmium, iron, nickel, radium, uranium, cobalt, lead, manganese, or arsenic.
 6. The method of claim 1, wherein the structures comprise an inert glass or ceramic material.
 7. The method of claim 1, wherein the structures comprise an organic material having an irregular shape.
 8. The method of claim 1, wherein the bacteria comprise at least one of the following: Deinococcus geothermalis, Deinococcus radiodurans, Vibrio proteolyticus, Shewanella piezotolerans, Shewanella Baltica, Pantoea agglomerans, Vibrio vulnificus and a combination thereof.
 9. The method of claim 1, wherein: the biofilm comprises bacteria and a matrix; and the matrix comprises a negatively charged material that attracts positive metal ions of the heavy metal and draws the metal into the matrix.
 10. The method of claim 1, wherein the passing comprises flowing the fracture fluid through the vessel at a flow rate that causes the fluid to be exposed to the biofilm for about 8 to about 10 minutes.
 11. A reactor vessel for treating fracture fluid from hydraulic fracturing comprising: a vessel; an inlet configured to receive fracture fluid into the vessel a biofilm retaining structure contained within the vessel; and a biofilm covering a substantial portion of the retaining structure, the biofilm comprising a bacteria and a matrix that will remove a heavy metal from the fracture fluid; and an outlet configured to expel treated fracture fluid from the vessel; wherein the inlet, the outlet, the biofilm retaining structure and the biofilm are configured so that the fracture fluid is uniformly exposed to the biofilm while in the vessel.
 12. The reactor vessel of claim 11, further comprising: an outlet tube connected to the outlet; and a one-way valve connected to the outlet tube and positioned to prevent re-entry of the fluid into the outlet tube after the fluid passes through the valve.
 13. The reactor vessel of claim 11, wherein the heavy metal comprises cadmium, iron, nickel, radium, uranium, cobalt, lead, manganese, arsenic or a combination thereof.
 14. The reactor vessel of claim 11, wherein the bacteria comprise at least one of the following: Deinococcus geothermalis, Deinococcus radiodurans, Vibrio proteolyticus, Shewanella piezotolerans, Shewanella Baltica, Pantoea agglomerans, Vibrio vulnificus and a combination thereof.
 15. The reactor vessel of claim 11, further comprising a flow regulator that limits the flow rate of the fluid into the vessel.
 16. The reactor vessel of claim 11 wherein the structures comprise an inert glass or ceramic material.
 17. The reactor vessel of claim 11 wherein the structures comprise an organic material having an irregular shape.
 18. The reactor vessel of claim 11, wherein the matrix comprises a negatively charged material that attracts positive metal ions of the heavy metal and draws the metal into the matrix. 